[ensembl-dev] Error during query execution using Refseq mRNA IDs as Filter

[Rhoda Kinsella]

Hi Johannes
I am glad that the workaround is okay but please let me know if you  
would like me to generate the results for you and I will do so.
Regards
Rhoda


On 7 Oct 2011, at 16:19, Johannes Meisig wrote:

> Hi Rhoda,
>
> thanks for answering so quickly! As a workaround, I make the  
> database query the other way around. It's a bit slower because I  
> have to plug in the whole genome now, but that's not a big problem.
>
> Johannes
>
> Rhoda Kinsella wrote:
>> Hi Johannes
>> This is a known bug (please see here: http://www.ensembl.info/contact-us/known-bugs/) 
>> . This known bugs page includes a temporary workaround.  
>> Unfortunately we will not be able to make the bug fix live until  
>> our next release 65 due out in November. I have, however, fixed  
>> this on an internal server and am happy to run your query for you  
>> if you send me your list of query RefSeq IDs. I hope that helps,
>> Regards
>> Rhoda
>> On 6 Oct 2011, at 15:16, Johannes Meisig wrote:
>>> Hi,
>>>
>>> a month I started using Ensembl/Biomart to find Ensembl Gene IDs
>>> corresponding to Refseq IDs. When I tried it again yesterday it  
>>> didn't
>>> work anymore.
>>>
>>> Selecting Ensembl Gene ID and Ensembl Transcript ID as attributes  
>>> and
>>> Refseq mRNA ID with the Mus musculus genes dataset I get the error
>>> attached to this message on the website.
>>>
>>> The error can be easily reproduced by plugging in the example ID
>>> NM_01195597 into the ID list. Is this problem known? Is there  
>>> anything I
>>> should do differently?
>>>
>>> Thanks,
>>> Johannes
>>>
>>> Serious Error: Error during query execution: Table
>>> 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
>>>
>>> ERROR: caught BioMart::Exception::Database: Error during query
>>> execution: Table 'ensembl_mart_64.ox_RefSeq_mRNA__dm' doesn't exist
>>>
>>> If you repeatedly get directed to this error page, there may be a
>>> problem with your current session parameters. To clear your  
>>> session and
>>> start with a clean slate, please click the New button below.
>>>
>>> Stacktrace:
>>> Exception::Class::Base::throw
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/ 
>>> TableSet.pm:241
>>> BioMart::Dataset::TableSet::_fillAttributeTableWith
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Dataset/ 
>>> TableSet.pm:124
>>> BioMart::Dataset::TableSet::_getResultTable
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/DatasetI.pm:1170
>>> BioMart::DatasetI::getResultTable
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm: 
>>> 472
>>> BioMart::QueryRunner::_processPath
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm: 
>>> 374
>>> BioMart::QueryRunner::_getResultTable
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/QueryRunner.pm: 
>>> 194
>>> BioMart::QueryRunner::execute
>>> /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm:2464
>>> (eval) /ensemblweb/wwwmart/www_64/biomart-perl/lib/BioMart/Web.pm: 
>>> 2216
>>> BioMart::Web::handle_request
>>> /ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:100
>>> (eval) /ensemblweb/wwwmart/www_64/biomart-perl/cgi-bin/martview:99
>>> ModPerl 
>>> ::ROOT 
>>> ::ModPerl 
>>> ::Registry 
>>> ::ensemblweb_wwwmart_www_64_biomart_2dperl_cgi_2dbin_martview 
>>> ::handler
>>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ 
>>> ModPerl/RegistryCooker.pm:204
>>> (eval)
>>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ 
>>> ModPerl/RegistryCooker.pm:204
>>> ModPerl::RegistryCooker::run
>>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ 
>>> ModPerl/RegistryCooker.pm:170
>>> ModPerl::RegistryCooker::default_handler
>>> /localsw/lib/perl5/site_perl/5.8.9/x86_64-linux-thread-multi/ 
>>> ModPerl/Registry.pm:31
>>> ModPerl::Registry::handler -e:0
>>> (eval) -e:0
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
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>>> Ensembl Blog: http://www.ensembl.info/
>> Rhoda Kinsella Ph.D.
>> Ensembl Production Project Leader,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus, Hinxton
>> Cambridge CB10 1SD,
>> UK.

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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